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Accepted version

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2017-11-01

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cc-by-nc-nd (c) Elsevier B.V., 2017
Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/127908

Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations

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https://doi.org/10.1016/j.jmgm.2017.10.005

Abstract

In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intraand intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetami de. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C-7(eq) only sampled in chloroform; the C-5 or extended conformation; the polyproline (PII) conformation and the right-handed alpha-helix conformation (alpha(R)). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed. (C) 2017 Elsevier Inc. All rights reserved.

Subject

Pèptids, Anàlisi conformacional, Solucions (Química)

Subject (English)

Peptides, Conformational analysis, Solution (Chemistry)

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Articles publicats en revistes (Ciència dels Materials i Química Física)
Articles publicats en revistes (Institut de Química Teòrica i Computacional (IQTCUB))

Citation

RUBIO MARTÍNEZ, Jaime, SANTOS TOMAS, M. and PEREZ, Juan J. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations. Journal of Molecular Graphics & Modelling. 2017. Vol. 78, num. 118-128. ISSN 1093-3263. [consulted: 19 of August of 2026]. Available at: https://hdl.handle.net/2445/127908

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